Mercurial > repos > ulfschaefer > phephenix
comparison Galaxy-Workflow-Phenix_workflow.ga @ 7:6ee955e652e0 draft
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| author | ulfschaefer |
|---|---|
| date | Wed, 27 Apr 2016 10:06:16 -0400 |
| parents | |
| children |
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| 6:e713aacaad05 | 7:6ee955e652e0 |
|---|---|
| 1 { | |
| 2 "a_galaxy_workflow": "true", | |
| 3 "annotation": "", | |
| 4 "format-version": "0.1", | |
| 5 "name": "Phenix workflow", | |
| 6 "steps": { | |
| 7 "0": { | |
| 8 "annotation": "", | |
| 9 "content_id": null, | |
| 10 "id": 0, | |
| 11 "input_connections": {}, | |
| 12 "inputs": [ | |
| 13 { | |
| 14 "description": "", | |
| 15 "name": "ref fa" | |
| 16 } | |
| 17 ], | |
| 18 "label": null, | |
| 19 "name": "Input dataset", | |
| 20 "outputs": [], | |
| 21 "position": { | |
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| 26 "tool_id": null, | |
| 27 "tool_state": "{\"name\": \"ref fa\"}", | |
| 28 "tool_version": null, | |
| 29 "type": "data_input", | |
| 30 "uuid": "b7ff9ad4-b07e-4c50-a38e-de10113b7314", | |
| 31 "workflow_outputs": [] | |
| 32 }, | |
| 33 "1": { | |
| 34 "annotation": "", | |
| 35 "content_id": null, | |
| 36 "id": 1, | |
| 37 "input_connections": {}, | |
| 38 "inputs": [ | |
| 39 { | |
| 40 "description": "", | |
| 41 "name": "r1" | |
| 42 } | |
| 43 ], | |
| 44 "label": null, | |
| 45 "name": "Input dataset", | |
| 46 "outputs": [], | |
| 47 "position": { | |
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| 49 "top": 273.5 | |
| 50 }, | |
| 51 "tool_errors": null, | |
| 52 "tool_id": null, | |
| 53 "tool_state": "{\"name\": \"r1\"}", | |
| 54 "tool_version": null, | |
| 55 "type": "data_input", | |
| 56 "uuid": "730623b2-2780-4de8-aa64-20949d734754", | |
| 57 "workflow_outputs": [] | |
| 58 }, | |
| 59 "2": { | |
| 60 "annotation": "", | |
| 61 "content_id": null, | |
| 62 "id": 2, | |
| 63 "input_connections": {}, | |
| 64 "inputs": [ | |
| 65 { | |
| 66 "description": "", | |
| 67 "name": "r2" | |
| 68 } | |
| 69 ], | |
| 70 "label": null, | |
| 71 "name": "Input dataset", | |
| 72 "outputs": [], | |
| 73 "position": { | |
| 74 "left": 209, | |
| 75 "top": 406.5 | |
| 76 }, | |
| 77 "tool_errors": null, | |
| 78 "tool_id": null, | |
| 79 "tool_state": "{\"name\": \"r2\"}", | |
| 80 "tool_version": null, | |
| 81 "type": "data_input", | |
| 82 "uuid": "f7d572ac-c3fc-4bb1-97fc-641460c32139", | |
| 83 "workflow_outputs": [] | |
| 84 }, | |
| 85 "3": { | |
| 86 "annotation": "", | |
| 87 "content_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.2", | |
| 88 "id": 3, | |
| 89 "input_connections": { | |
| 90 "fastq_input|fastq_input1": { | |
| 91 "id": 1, | |
| 92 "output_name": "output" | |
| 93 }, | |
| 94 "fastq_input|fastq_input2": { | |
| 95 "id": 2, | |
| 96 "output_name": "output" | |
| 97 }, | |
| 98 "reference_source|ref_file": { | |
| 99 "id": 0, | |
| 100 "output_name": "output" | |
| 101 } | |
| 102 }, | |
| 103 "inputs": [], | |
| 104 "label": null, | |
| 105 "name": "Map with BWA-MEM", | |
| 106 "outputs": [ | |
| 107 { | |
| 108 "name": "bam_output", | |
| 109 "type": "bam" | |
| 110 } | |
| 111 ], | |
| 112 "position": { | |
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| 114 "top": 203.5 | |
| 115 }, | |
| 116 "post_job_actions": {}, | |
| 117 "tool_errors": null, | |
| 118 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.4.2", | |
| 119 "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1}\"}", | |
| 120 "tool_version": "0.4.2", | |
| 121 "type": "tool", | |
| 122 "uuid": "1896896c-a5c5-408b-8f43-54fb3d466e59", | |
| 123 "workflow_outputs": [] | |
| 124 }, | |
| 125 "4": { | |
| 126 "annotation": "", | |
| 127 "content_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", | |
| 128 "id": 4, | |
| 129 "input_connections": { | |
| 130 "input_bam": { | |
| 131 "id": 3, | |
| 132 "output_name": "bam_output" | |
| 133 }, | |
| 134 "ref_file": { | |
| 135 "id": 0, | |
| 136 "output_name": "output" | |
| 137 } | |
| 138 }, | |
| 139 "inputs": [], | |
| 140 "label": null, | |
| 141 "name": "PHE MPileup", | |
| 142 "outputs": [ | |
| 143 { | |
| 144 "name": "outvcf", | |
| 145 "type": "vcf" | |
| 146 } | |
| 147 ], | |
| 148 "position": { | |
| 149 "left": 456, | |
| 150 "top": 425.5 | |
| 151 }, | |
| 152 "post_job_actions": {}, | |
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| 154 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", | |
| 155 "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}", | |
| 156 "tool_version": "1.0", | |
| 157 "type": "tool", | |
| 158 "uuid": "dd975120-5a22-467b-a8f7-cc801faccfd6", | |
| 159 "workflow_outputs": [] | |
| 160 }, | |
| 161 "5": { | |
| 162 "annotation": "", | |
| 163 "content_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", | |
| 164 "id": 5, | |
| 165 "input_connections": { | |
| 166 "input": { | |
| 167 "id": 4, | |
| 168 "output_name": "outvcf" | |
| 169 } | |
| 170 }, | |
| 171 "inputs": [], | |
| 172 "label": null, | |
| 173 "name": "Filter VCF", | |
| 174 "outputs": [ | |
| 175 { | |
| 176 "name": "output", | |
| 177 "type": "vcf" | |
| 178 } | |
| 179 ], | |
| 180 "position": { | |
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| 184 "post_job_actions": {}, | |
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| 186 "tool_id": "testtoolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", | |
| 187 "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"gq_score\\\": \\\"0\\\", \\\"__current_case__\\\": 0, \\\"snp_filter_type_selector\\\": \\\"gq_score_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}]\", \"__page__\": 0}", | |
| 188 "tool_version": "1.0", | |
| 189 "type": "tool", | |
| 190 "uuid": "36480e46-74dd-4bb7-b350-c3e75f4f2354", | |
| 191 "workflow_outputs": [] | |
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| 194 "uuid": "15c9a48b-931d-4ff6-b12f-4c9a1affea2e" | |
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